Vibrational dependence of the H2-H2 C6 dispersion coefficients

We use the sum-over-states formalism to compute the imaginary-frequency dipole polarizabilities for H2, as a function of the H-H bond length, at the full configuration interaction level of theory using atom-centered d-aug-cc-pVQZ basis sets. From these polarizabilities, we obtain isotropic and anisotropic C6 dispersion coefficients for a pair of H2 molecules as functions of the two molecules' bond lengths.     

Chaotic dynamics and vibrational mode coupling in small argon clusters

We have computed the local Kolmogorov entropy of molecular dynamics trajectory segments near the potential energy saddles of model Ar₃ and Ar₅ clusters. In the case of Ar₃ clusters bound with a Lennard-Jones potential, the local Kolmogorov entropy of the cluster is significantly smaller in the saddle region than in other areas of the potential surface. This behavior indicates an increase in the degree of nearly quasiperiodic motion near the Ar₃ saddle due to the partial decoupling of the cluster's vibrational modes there. Lennard-Jones Ar₅ clusters do not exhibit similar behavior, but Ar₅ clusters bound with a short-range Morse potential do. This suggests that the “regularizing” effect of saddle regions is strongly dependent on the shape of the energy surface near the saddle. From these observations, we can determine which features of the saddle are most important in this respect; the flatness of the saddle region seems to be one such feature.     

A preference for edgewise interactions between aromatic rings and carboxylate anions: the biological relevance of anion-quadrupole interactions

Noncovalent interactions are quite important in biological structure-function relationships. To study the pairwise interaction of aromatic amino acids (phenylalanine, tyrosine, tryptophan) with anionic amino acids (aspartic and glutamic acids), small molecule mimics (benzene, phenol or indole interacting with formate) were used at the MP2 level of theory. The overall energy associated with an anion-quadrupole interaction is substantial (-9.5 kcal/mol for a benzene-formate planar dimer at van der Waals contact distance), indicating the electropositive ring edge of an aromatic group can interact with an anion. Deconvolution of the long-range coplanar interaction energy into fractional contributions from charge-quadrupole interactions, higher-order electrostatic interactions, and polarization terms was achieved. The charge-quadrupole term contributes between 30 to 45% of the total MP2 benzene-formate interaction; most of the rest of the interaction arises from polarization contributions. Additional studies of the Protein Data Bank (PDB Select) show that nearly planar aromatic-anionic amino acid pairs occur more often than expected from a random angular distribution, while axial aromatic-anionic pairs occur less often than expected; this demonstrates the biological relevance of the anion-quadrupole interaction. While water may mitigate the strength of these interactions, they may be numerous in a typical protein structure, so their cumulative effect could be substantial.     

Nanofabricated periodic arrays of silver elliptical discs as SERS substrates

Signal enhancement observed in surface‐enhanced Raman spectroscopy (SERS) is attributable to the presence of noble‐metal nanostructures on substrate surfaces. The rational development of SERS‐active substrates depends critically on the homogeneity and intensity of surface plasmon resonances, properties that are strongly dependent on both the morphology and dielectric properties of the metals and composite materials making up the SERS substrates. Enhancement can be controlled by the shape, size, and spacing of metallic nanoparticles. Previous studies in our group have shown that arrays of elliptical nanodiscs have promising geometries for this purpose. Using electron beam lithography (EBL), we fabricate close‐packed arrays of these discs with lateral dimensions ranging from 300:50 to 300:300 nm (long axis : short axis). The arrays are composed of a negative photoresist that, once the lithography process is complete, are coated with a noble metal through physical vapor deposition (PVD). In this work, optimum thickness and deposition rate of noble metal are determined for these substrates. The lithographically produced nanopatterns are studied by Raman spectroscopy to examine the effect of altering the elliptical aspect ratio on SERS activity, while scanning electron microscopy (SEM) is used to examine pattern surfaces post lithographic development and post noble‐metal deposition. Atomic force microscopy (AFM) is used to inspect the roughness of substrate surfaces. Reproducibility between different arrays of the same pattern ranges from 12 to 28%. Homogeneity of our uniform‐morphology EBL/PVD‐fabricated substrates is examined and compared to our random‐morphology polymer nanocomposite substrates. Using rhodamine 6G as an analyte, an increase in SERS signal is noted as the aspect ratio of ellipses goes from 6:1 to 6:6. Our experimental data, in terms of trends in SERS activity, correlate with trends in field enhancements calculated using a simple electrostatic model and with the magnitude of the broad red‐shifted spectral continuum observed for the substrates. Copyright © 2008 John Wiley & Sons, Ltd.     

An ab initio study of van der Waals potential energy parameters for silver clusters

We employ ab initio calculations of van der Waals complexes to study the potential energy parameters (C(6) coefficients) of van der Waals interactions for modeling of the adsorption of silver clusters on the graphite surface. Electronic structure calculations of the (Ag(2))(2), Ag(2)-H(2), and Ag(2)-C(6)H(6) complexes are performed using a coupled-cluster approach that includes single, double, and perturbative triple excitations (CCSD(T)), M?ller-Plesset second-order perturbation theory (MP2), and spin-component-scaled MP2 (SCS-MP2) methods. Using the atom pair approximation, the C(6) coefficients for silver-silver, silver-hydrogen, and silver-carbon atom systems are obtained after subtracting the energies of quadrupole-quadrupole interactions from the total electronic energy.     

Enthalpies of formation and bond dissociation energies of lower alkyl hydroperoxides and related hydroperoxy and alkoxy radicals

The enthalpies of formation and bond dissociation energies, D(ROO-H), D(RO-OH), D(RO-O), D(R-O 2) and D(R-OOH) of alkyl hydroperoxides, ROOH, alkyl peroxy, RO, and alkoxide radicals, RO, have been computed at CBS-QB3 and APNO levels of theory via isodesmic and atomization procedures for R = methyl, ethyl, n-propyl and isopropyl and n-butyl, tert-butyl, isobutyl and sec-butyl. We show that D(ROO-H) approximately 357, D(RO-OH) approximately 190 and D(RO-O) approximately 263 kJ mol (-1) for all R, whereas both D(R-OO) and D(R-OOH) strengthen with increasing methyl substitution at the alpha-carbon but remain constant with increasing carbon chain length. We recommend a new set of group additivity contributions for the estimation of enthalpies of formation and bond energies.     

Angstrom-to-millimeter characterization of sedimentary rock microstructure

Backscatter SEM imaging and small-angle neutron scattering (SANS) data are combined within a statistical framework to quantify the microstructure of a porous solid in terms of a continuous pore-size distribution spanning over five orders of magnitude of length scale, from 10 A to 500 microm. The method is demonstrated on a sample of natural sandstone and the results are tested against mercury porosimetry (MP) and nuclear magnetic resonance (NMR) relaxation data. The rock microstructure is fractal (D=2.47) in the pore-size range 10 A-50 microm and Euclidean for larger length scales. The pore-size distribution is consistent with that determined by MP. The NMR data show a bimodal distribution of proton T(2) relaxation times, which is interpreted quantitatively using a model of relaxation in fractal pores. Pore-length scales derived from the NMR data are consistent with the geometrical parameters derived from both the SEM/SANS and MP data. The combined SANS/BSEM method furnishes new microstructural information that should facilitate the study of capillary phenomena in hydrocarbon reservoir rocks and other porous solids exhibiting broad pore-size distributions.     

Quantum dynamics of rovibrational transitions in H2-H2 collisions: internal energy and rotational angular momentum conservation effects

We present a full dimensional quantum mechanical treatment of collisions between two H(2) molecules over a wide range of energies. Elastic and state-to-state inelastic cross sections for ortho-H(2)?+ para-H(2) and ortho-H(2)?+ ortho-H(2) collisions have been computed for different initial rovibrational levels of the molecules. For rovibrationally excited molecules, it has been found that state-to-state transitions are highly specific. Inelastic collisions that conserve the total rotational angular momentum of the diatoms and that involve small changes in the internal energy are found to be highly efficient. The effectiveness of these quasiresonant processes increases with decreasing collision energy and they become highly state-selective at ultracold temperatures. They are found to be more dominant for rotational energy exchange than for vibrational transitions. For non-reactive collisions between ortho- and para-H(2) molecules for which rotational energy exchange is forbidden, the quasiresonant mechanism involves a purely vibrational energy transfer albeit with less efficiency. When inelastic collisions are dominated by a quasiresonant transition calculations using a reduced basis set involving only the quasiresonant channels yield nearly identical results as the full basis set calculation leading to dramatic savings in computational cost.